| Year |
Citation |
Score |
| 2019 |
Almeida JS, Hajagos J, Saltz J, Saltz M. Serverless OpenHealth at data commons scale-traversing the 20 million patient records of New York's SPARCS dataset in real-time. Peerj. 7: e6230. PMID 30671301 DOI: 10.7717/Peerj.6230 |
0.307 |
|
| 2018 |
Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, ... ... Almeida JS, et al. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. Plos Biology. 16: e3000099. PMID 30596645 DOI: 10.1371/Journal.Pbio.3000099 |
0.315 |
|
| 2018 |
Dussaq AM, Kennell T, Eustace NJ, Anderson JC, Almeida JS, Willey CD. Kinomics toolbox-A web platform for analysis and viewing of kinomic peptide array data. Plos One. 13: e0202139. PMID 30130366 DOI: 10.1371/Journal.Pone.0202139 |
0.331 |
|
| 2017 |
Zielezinski A, Vinga S, Almeida J, Karlowski WM. Alignment-free Sequence Comparison: Benefits, Applications, and Tools Genome Biology. 18: 186-186. PMID 28974235 DOI: 10.1186/S13059-017-1319-7 |
0.324 |
|
| 2016 |
Penha ED, Iriabho E, Dussaq A, de Oliveira DM, Almeida JS. Isomorphic semantic mapping of variant call format (VCF2RDF). Bioinformatics (Oxford, England). PMID 27797761 DOI: 10.1093/Bioinformatics/Btw652 |
0.338 |
|
| 2014 |
Wilkinson SR, Almeida JS. QMachine: commodity supercomputing in web browsers. Bmc Bioinformatics. 15: 176. PMID 24913605 DOI: 10.1186/1471-2105-15-176 |
0.318 |
|
| 2014 |
Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. Bmc Bioinformatics. 15: 28. PMID 24467687 DOI: 10.1186/1471-2105-15-28 |
0.335 |
|
| 2014 |
Almeida JS. Sequence analysis by iterated maps, a review. Briefings in Bioinformatics. 15: 369-75. PMID 24162172 DOI: 10.1093/Bib/Bbt072 |
0.32 |
|
| 2013 |
Robbins DE, Grüneberg A, Deus HF, Tanik MM, Almeida JS. A self-updating road map of The Cancer Genome Atlas. Bioinformatics (Oxford, England). 29: 1333-40. PMID 23595662 DOI: 10.1093/Bioinformatics/Btt141 |
0.315 |
|
| 2013 |
Kim YW, Koul D, Kim SH, Lucio-Eterovic AK, Freire PR, Yao J, Wang J, Almeida JS, Aldape K, Yung WK. Identification of prognostic gene signatures of glioblastoma: a study based on TCGA data analysis. Neuro-Oncology. 15: 829-39. PMID 23502430 DOI: 10.1093/Neuonc/Not024 |
0.315 |
|
| 2012 |
Almeida JS, Iriabho EE, Gorrepati VL, Wilkinson SR, Grüneberg A, Robbins DE, Hackney JR. ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser. Journal of Pathology Informatics. 3: 25. PMID 22934238 DOI: 10.4103/2153-3539.98813 |
0.302 |
|
| 2012 |
Almeida JS, Grüneberg A, Maass W, Vinga S. Fractal MapReduce decomposition of sequence alignment. Algorithms For Molecular Biology : Amb. 7: 12. PMID 22551205 DOI: 10.1186/1748-7188-7-12 |
0.333 |
|
| 2012 |
Vinga S, Carvalho AM, Francisco AP, Russo LM, Almeida JS. Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. Algorithms For Molecular Biology : Amb. 7: 10. PMID 22551152 DOI: 10.1186/1748-7188-7-10 |
0.317 |
|
| 2011 |
Deus HF, Correa MC, Stanislaus R, Miragaia M, Maass W, de Lencastre H, Fox R, Almeida JS. S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. Bmc Bioinformatics. 12: 285. PMID 21756325 DOI: 10.1186/1471-2105-12-285 |
0.327 |
|
| 2010 |
Correa MC, Deus HF, Vasconcelos AT, Hayashi Y, Ajani JA, Patnana SV, Almeida JS. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services. Bmc Medical Informatics and Decision Making. 10: 65. PMID 20977768 DOI: 10.1186/1472-6947-10-65 |
0.308 |
|
| 2010 |
Almeida JS. Computational ecosystems for data-driven medical genomics. Genome Medicine. 2: 67. PMID 20854645 DOI: 10.1186/Gm188 |
0.316 |
|
| 2010 |
Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS. Exposing the cancer genome atlas as a SPARQL endpoint. Journal of Biomedical Informatics. 43: 998-1008. PMID 20851208 DOI: 10.1016/J.Jbi.2010.09.004 |
0.339 |
|
| 2010 |
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics. 10: 3073-81. PMID 20677327 DOI: 10.1002/Pmic.201000120 |
0.313 |
|
| 2010 |
Almeida JS, Deus HF, Maass W. S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. Bmc Bioinformatics. 11: 387. PMID 20646315 DOI: 10.1186/1471-2105-11-387 |
0.345 |
|
| 2008 |
Freire P, Vilela M, Deus H, Kim YW, Koul D, Colman H, Aldape KD, Bogler O, Yung WK, Coombes K, Mills GB, Vasconcelos AT, Almeida JS. Exploratory analysis of the copy number alterations in glioblastoma multiforme. Plos One. 3: e4076. PMID 19115005 DOI: 10.1371/Journal.Pone.0004076 |
0.3 |
|
| 2008 |
Stanislaus R, Carey M, Deus HF, Coombes K, Hennessy BT, Mills GB, Almeida JS. RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays. Bmc Bioinformatics. 9: 555. PMID 19102773 DOI: 10.1186/1471-2105-9-555 |
0.338 |
|
| 2008 |
Deus HF, Stanislaus R, Veiga DF, Behrens C, Wistuba II, Minna JD, Garner HR, Swisher SG, Roth JA, Correa AM, Broom B, Coombes K, Chang A, Vogel LH, Almeida JS. A Semantic Web management model for integrative biomedical informatics. Plos One. 3: e2946. PMID 18698353 DOI: 10.1371/Journal.Pone.0002946 |
0.301 |
|
| 2008 |
Robinson CJ, Swift S, Johnson DD, Almeida JS. Prediction of pelvic organ prolapse using an artificial neural network. American Journal of Obstetrics and Gynecology. 199: 193.e1-6. PMID 18533119 DOI: 10.1016/J.Ajog.2008.04.029 |
0.315 |
|
| 2008 |
Stanislaus R, Arthur JM, Rajagopalan B, Moerschell R, McGlothlen B, Almeida JS. An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. Bmc Bioinformatics. 9: 4. PMID 18179696 DOI: 10.1186/1471-2105-9-4 |
0.361 |
|
| 2007 |
Vinga S, Almeida JS. Local Renyi entropic profiles of DNA sequences. Bmc Bioinformatics. 8: 393. PMID 17939871 DOI: 10.1186/1471-2105-8-393 |
0.306 |
|
| 2007 |
Karpievitch YV, Hill EG, Smolka AJ, Morris JS, Coombes KR, Baggerly KA, Almeida JS. PrepMS: TOF MS data graphical preprocessing tool. Bioinformatics (Oxford, England). 23: 264-5. PMID 17121773 DOI: 10.1093/Bioinformatics/Btl583 |
0.322 |
|
| 2007 |
Garcia SP, Delancey LB, Almeida JS, Chapman RW. Ecoforecasting in real time for commercial fisheries: The Atlantic white shrimp as a case study Marine Biology. 152: 15-24. DOI: 10.1007/S00227-007-0622-3 |
0.31 |
|
| 2006 |
Geli P, Rolfhamre P, Almeida J, Ekdahl K. Modeling Pneumococcal Resistance to Penicillin in Southern Sweden Using Artificial Neural Networks Microbial Drug Resistance. 12: 149-157. PMID 17002540 DOI: 10.1089/Mdr.2006.12.149 |
0.301 |
|
| 2005 |
Wang X, Gorlitsky R, Almeida JS. From XML to RDF: how semantic web technologies will change the design of 'omic' standards. Nature Biotechnology. 23: 1099-103. PMID 16151403 DOI: 10.1038/Nbt1139 |
0.324 |
|
| 2005 |
McKillen DJ, Chen YA, Chen C, Jenny MJ, Trent HF, Robalino J, McLean DC, Gross PS, Chapman RW, Warr GW, Almeida JS. Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. Bmc Genomics. 6: 34. PMID 15760464 DOI: 10.1186/1471-2164-6-34 |
0.303 |
|
| 2005 |
Stanislaus R, Chen C, Franklin J, Arthur J, Almeida JS. AGML Central: web based gel proteomic infrastructure. Bioinformatics (Oxford, England). 21: 1754-7. PMID 15647304 DOI: 10.1093/Bioinformatics/Bti246 |
0.334 |
|
| 2005 |
Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method. Bioinformatics (Oxford, England). 21: 1037-45. PMID 15509607 DOI: 10.1093/Bioinformatics/Bti074 |
0.329 |
|
| 2004 |
Chen YA, McKillen DJ, Wu S, Jenny MJ, Chapman R, Gross PS, Warr GW, Almeida JS. Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. Bmc Bioinformatics. 5: 191. PMID 15585062 DOI: 10.1186/1471-2105-5-191 |
0.302 |
|
| 2004 |
Stanislaus R, Jiang LH, Swartz M, Arthur J, Almeida JS. An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. Bmc Bioinformatics. 5: 9. PMID 15005801 DOI: 10.1186/1471-2105-5-9 |
0.344 |
|
| 2004 |
Vinga S, Gouveia-Oliveira R, Almeida JS. Comparative evaluation of word composition distances for the recognition of SCOP relationships. Bioinformatics (Oxford, England). 20: 206-15. PMID 14734312 DOI: 10.1093/Bioinformatics/Btg392 |
0.306 |
|
| 2003 |
Almeida JS, Voit EO. Neural-network-based parameter estimation in S-system models of biological networks. Genome Informatics. International Conference On Genome Informatics. 14: 114-23. PMID 15706526 DOI: 10.11234/Gi1990.14.114 |
0.357 |
|
| 2002 |
Schwacke J, Almeida JS. Efficient Boolean implementation of universal sequence maps (bUSM). Bmc Bioinformatics. 3: 28-28. PMID 12387731 DOI: 10.1186/1471-2105-3-28 |
0.306 |
|
| 2002 |
Almeida JS. Predictive non-linear modeling of complex data by artificial neural networks Current Opinion in Biotechnology. 13: 72-76. PMID 11849962 DOI: 10.1016/S0958-1669(02)00288-4 |
0.332 |
|
| 2001 |
Almeida JS, Carriço JA, Maretzek A, Noble PA, Fletcher M. Analysis of genomic sequences by Chaos Game Representation Bioinformatics. 17: 429-437. PMID 11331237 DOI: 10.1093/Bioinformatics/17.5.429 |
0.333 |
|
| 2001 |
Wolf G, Almeida JS, Pinheiro C, Correia V, Rodrigues C, Reis MAM, Crespo JG. Two-dimensional fluorometry coupled with artificial neural networks: A novel method for on-line monitoring of complex biological processes Biotechnology and Bioengineering. 72: 297-306. PMID 11135199 DOI: 10.1002/1097-0290(20010205)72:3<297::Aid-Bit6>3.0.Co;2-B |
0.302 |
|
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